Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,610,194 C→T 9.5% P227P (CCC→CCT)  PP_4081 → type IV/VI secretion system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,610,1940CT 9.5% 111.4 / 3.1 42P227P (CCC→CCT) PP_4081type IV/VI secretion system protein
Reads supporting (aligned to +/- strand):  ref base C (19/19);  new base T (2/2);  total (21/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.09e-01

TCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGA  >  NC_002947/4610056‑4610342
                                                                                                                                          |                                                                                                                                                     
tCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCgaa                                                                                                                                              <  6:238608/148‑1 (MQ=37)
 cAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAc                                                                                                                                                     >  8:288199/1‑140 (MQ=37)
 cAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAc                                                                                                                                                     <  7:288199/140‑1 (MQ=37)
    gACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAccccc                                                                                                                                                 <  6:42783/141‑1 (MQ=37)
    gACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAccccc                                                                                                                                                 >  5:42783/1‑141 (MQ=37)
     aCGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTc                                                                                                                                        <  4:101255/149‑1 (MQ=37)
            ggAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGAcc                                                                                                                                 >  6:220116/1‑149 (MQ=37)
             gAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGAccc                                                                                                                                <  2:181546/149‑1 (MQ=37)
               gagcgcgtacttgcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGAcccc                                                                                                                               >  5:113793‑M2/44‑148 (MQ=255)
                   gcgtacttgcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGAcc                                                                                                                                 >  4:127155‑M2/40‑142 (MQ=255)
                   gcgtacttgcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGAcc                                                                                                                                 <  3:127155‑M2/103‑1 (MQ=255)
                           gcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGACCCC‑TACACCAATGt                                                                                                                   <  6:113793‑M2/116‑1 (MQ=255)
                                  tgCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCa                                                                                                           <  2:82645/148‑1 (MQ=255)
                                        gggCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGCAGTATGCGCCCCA‑TACACCAACGTCGCCCCCAGAAACtt                                                                                                    >  2:96354/1‑149 (MQ=255)
                                          gCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCTAAGAAGTCTGCTACCCC‑TACACCAACGTCGCCCCCAGAAACTTcc                                                                                                  <  6:150388/149‑1 (MQ=255)
                                          gCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTcc                                                                                                  <  8:55153/149‑1 (MQ=255)
                                                  gCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGc                                                                                          >  3:237879/1‑149 (MQ=255)
                                                         tGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCAt                                                                                              <  6:226065/138‑1 (MQ=255)
                                                            gcTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGc                                                                                >  4:199675/1‑149 (MQ=255)
                                                                   ccGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgtggtg                                                                         <  4:237879/149‑1 (MQ=255)
                                                                    cGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgtggtg                                                                         >  2:271734/1‑148 (MQ=255)
                                                                        aGGCGAAGAAACACTCAACGCACTGAATCACCAACTGCACGGGATCATCCGCGAACTGCTCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGc                                                                     <  1:96354/149‑1 (MQ=255)
                                                                          gCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGata                                                                                    <  1:211732/131‑1 (MQ=255)
                                                                          gCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCg                                                                  >  6:16426/1‑149 (MQ=255)
                                                                          gCGAAGAAACACTCAACGCACTCATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGata                                                                                    >  2:211732/1‑131 (MQ=255)
                                                                            gaagaaACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgt                                                                             <  2:101598/136‑1 (MQ=255)
                                                                            gaagaaACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgt                                                                             >  1:101598/1‑136 (MQ=255)
                                                                                  acacTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCAt                                                          <  1:271734/149‑1 (MQ=255)
                                                                                      tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGCCCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTcc                                                      >  8:242097/1‑149 (MQ=255)
                                                                                      tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCAt                                                                                              >  4:178000/1‑109 (MQ=255)
                                                                                      tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTcc                                                      >  8:33918/1‑149 (MQ=255)
                                                                                      tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGGGGTGGAGCCCGTTGGTCATCTcc                                                      >  8:193858/1‑149 (MQ=255)
                                                                                        aaCGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCcgc                                                    >  2:314184/1‑149 (MQ=255)
                                                                                        aaCGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCcgc                                                    >  2:319280/1‑149 (MQ=255)
                                                                                                 aTTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCcgccatcgcca                                            <  7:33918/148‑1 (MQ=255)
                                                                                                 aTTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGCTGGAGCCCGTAGGTCATCTCcgccaaagccat                                           >  8:245682/1‑149 (MQ=255)
                                                                                                     aCCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTAGGTCATCTCCGCCCTCGCCATGGCg                                       >  7:284262/1‑149 (MQ=255)
                                                                                                              aCGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTAc                              >  1:11990/1‑149 (MQ=255)
                                                                                                                gggATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACgg                            <  5:220116/149‑1 (MQ=255)
                                                                                                                    tcatcCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGAtt                        <  5:16426/149‑1 (MQ=255)
                                                                                                                      atcCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTa                      <  7:193858/149‑1 (MQ=255)
                                                                                                                        ccGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACa                    <  3:199675/149‑1 (MQ=255)
                                                                                                                                       ccccACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCAcc     <  1:314184/149‑1 (MQ=255)
                                                                                                                                       ccccACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCAcc     <  1:319280/149‑1 (MQ=255)
                                                                                                                                          cACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGa  >  3:13442/1‑149 (MQ=255)
                                                                                                                                          |                                                                                                                                                     
TCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGA  >  NC_002947/4610056‑4610342

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑